helmkit 0.7.1__tar.gz → 0.7.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {helmkit-0.7.1 → helmkit-0.7.2}/PKG-INFO +1 -1
- {helmkit-0.7.1 → helmkit-0.7.2}/pyproject.toml +1 -1
- {helmkit-0.7.1 → helmkit-0.7.2}/src/helmkit/molecule.py +40 -46
- {helmkit-0.7.1 → helmkit-0.7.2}/uv.lock +99 -105
- {helmkit-0.7.1 → helmkit-0.7.2}/.gitignore +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/.python-version +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/LICENSE +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/README.md +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/src/helmkit/__init__.py +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/src/helmkit/data/monomers.sdf +0 -0
- {helmkit-0.7.1 → helmkit-0.7.2}/src/helmkit/py.typed +0 -0
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@@ -7,6 +7,7 @@ from collections.abc import Callable
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from collections.abc import Sequence
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from functools import lru_cache
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from importlib.resources import files
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from typing import overload
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from typing import TypedDict
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from typing import TypeVar
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@@ -29,27 +30,36 @@ def get_molecule_property(
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T = TypeVar("T")
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@overload
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def parse_comma_separated_property(
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molecule: Chem.Mol, property_name: str, convert_func: None = None
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) -> list[str | None]: ...
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@overload
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def parse_comma_separated_property(
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molecule: Chem.Mol, property_name: str, convert_func: Callable[[str], T]
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) -> list[T | None]: ...
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def parse_comma_separated_property(
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molecule: Chem.Mol,
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property_name: str,
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convert_func: Callable[[str], T] | None = None,
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) ->
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) -> list[str | None] | list[T | None]:
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property_value = get_molecule_property(molecule, property_name)
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if not property_value:
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return []
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values = property_value.split(",")
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if convert_func:
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else
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values = [None if v == "None" else v for v in values]
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return values
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return [convert_func(v) if v != "None" else None for v in values]
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return [None if v == "None" else v for v in values]
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def infer_attachment_points(
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molecule: Chem.Mol, rgroup_indices: Sequence[int | None]
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) -> list[int]:
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) -> list[int | None]:
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"""Infer attachment points by finding atoms bonded to R-group atoms."""
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attachment_points = []
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@@ -75,9 +85,9 @@ def infer_attachment_points(
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class MonomerData(TypedDict):
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m_romol: Chem.Mol
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m_Rgroups: list[str]
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m_RgroupIdx: list[int]
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m_attachmentPointIdx: list[int]
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m_Rgroups: list[str | None]
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m_RgroupIdx: list[int | None]
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m_attachmentPointIdx: list[int | None]
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m_type: str
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m_subtype: str
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m_abbr: str
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@@ -267,16 +277,8 @@ class Molecule:
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def _parse_helm_string(self, helm: str) -> None:
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"""Parse a HELM string into molecular components."""
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if len(helm_parts) < 5:
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warnings.warn(f"Problem with HELM string - not enough sections: {helm}")
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return
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polymer_sections, connection_sections, hydrogen_bonds_sections = (
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helm_parts[0],
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helm_parts[1],
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helm_parts[2],
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polymer_sections, connection_sections, hydrogen_bonds_sections, _, _ = (
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self._split_helm_sections(helm)
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)
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if not polymer_sections:
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@@ -287,28 +289,21 @@ class Molecule:
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self._process_connections(connection_sections)
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self._process_hydrogen_bonds(hydrogen_bonds_sections)
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def _split_helm_sections(
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def _split_helm_sections(
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self, helm: str
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) -> tuple[list[str], list[str], list[str], str, str]:
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parts = self._dollar_outside_brackets.split(helm, 4)
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parts.extend([""] * (5 - len(parts)))
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polymers = (
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self._pipe_outside_brackets.split(parts[0])
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if "|" in parts[0]
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else [parts[0]]
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)
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connections = parts[1].split("|") if parts[1] else []
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hydrogen_bonds = parts[2].split("|") if parts[2] else []
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parts[1] = parts[1].split("|") if "|" in parts[1] else [parts[1]]
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else:
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parts[1] = []
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if parts[2]:
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parts[2] = parts[2].split("|") if "|" in parts[2] else [parts[2]]
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else:
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parts[2] = []
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return parts
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return polymers, connections, hydrogen_bonds, parts[3], parts[4]
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@staticmethod
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def _split_sequence_with_brackets(sequence: str) -> list[str]:
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return result
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def _extract_chain_id(self, chain_str: str) -> tuple[str
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"""Extract chain ID and
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def _extract_chain_id(self, chain_str: str) -> tuple[str, str]:
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"""Extract chain ID and return (chain_id, polymer_type)."""
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match = re.match(r"([A-Z]+)(\d+)", chain_str)
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if not match:
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return None, False, None
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raise ValueError(f"Invalid chain format: {chain_str}")
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polymer_type = match.group(1)
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if polymer_type not in
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return chain_str, True, polymer_type
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if polymer_type not in {"PEPTIDE", "RNA", "CHEM"}:
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raise ValueError(f"Unsupported polymer type: {polymer_type}")
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return chain_str, polymer_type
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def _process_monomer(
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self, monomer_name: str, chain_id: str, residue_idx: int, polymer_type: str
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continue
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id_chain = chain[: match.start()]
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chain_id,
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continue
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chain_id, polymer_type = self._extract_chain_id(id_chain)
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if chain_id in self.chain_offset:
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raise ValueError(f"Duplicate chain ID: {chain_id}")
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_monomer_df: MonomerLibrary | None = None
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def _init_pool(monomer_df: MonomerLibrary):
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global _monomer_df
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_monomer_df = monomer_df
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[[package]]
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name = "certifi"
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version = "2026.
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version = "2026.7.22"
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source = { registry = "https://pypi.org/simple" }
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sdist = { url = "https://files.pythonhosted.org/packages/a3/c2/24167ea9858356b47a87a50d39908bfdb72ceeefe0041586e704e5376b3a/certifi-2026.7.22.tar.gz", hash = "sha256:741e2c3b351ddf169a738da9f2c048608ff7f2c5cc02f1ebc6b118bb090d5d55", size = 138112, upload-time = "2026-07-22T03:35:12.644Z" }
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{ url = "https://files.pythonhosted.org/packages/
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{ url = "https://files.pythonhosted.org/packages/0b/a7/71ac2cff56fec219ed242bb11b8efb69fcc4bec75db06fb7bfe35de520e6/certifi-2026.7.22-py3-none-any.whl", hash = "sha256:62f22742b58a1a33014a2b6b706588a8d7e2a88ae7bd1a6ebe8c992928483775", size = 136983, upload-time = "2026-07-22T03:35:11.276Z" },
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name = "helmkit"
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version = "0.7.2"
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source = { editable = "." }
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dependencies = [
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name = "pandas"
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version = "3.0.5"
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dependencies = [
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{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" },
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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+
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701
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]
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[[package]]
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@@ -756,14 +750,14 @@ wheels = [
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[[package]]
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name = "tqdm"
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759
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-
version = "4.
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753
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+
version = "4.69.1"
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source = { registry = "https://pypi.org/simple" }
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dependencies = [
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{ name = "colorama", marker = "sys_platform == 'win32'" },
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]
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sdist = { url = "https://files.pythonhosted.org/packages/
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+
sdist = { url = "https://files.pythonhosted.org/packages/dd/84/da0e5038228fa34dfd77c5026b173ed035d2a3ba31f1077590c013de2bff/tqdm-4.69.1.tar.gz", hash = "sha256:2be21080a0ce17e902c2f1baeb6a74bf551b67bbdfa4bc0109fad471d0b4cb0d", size = 793046, upload-time = "2026-07-24T14:22:02.08Z" }
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/
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{ url = "https://files.pythonhosted.org/packages/01/50/5817619a0fca56aff06383dbfde7ae017b3ca383915b3f1e4713164273cf/tqdm-4.69.1-py3-none-any.whl", hash = "sha256:0a654b96f7a2660cceb615b56f307ec2bef96c515409014a429a561981ab52b4", size = 675452, upload-time = "2026-07-24T14:22:00.048Z" },
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